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<h1 align="center">Structure Building</h1>

<p align="left">

The structure building panel is designed to handle multiple structures
at the same time. Initially the structure panel is empty. The user can
start building a structure from a common core motif selected from the
&quot;File -> New&quot; menu. To add subsequent structures using one
of the core motifs the user can chose from the &quot;Structure -> Add
structure&quot; menu. 

<br><br>

Only tree-like glycan structures can be built. The residues are always
added to the last selected residue. If no residue is selected a new
structure is created and the residue is added to it. The substituents
are treated as residues. A new residue is added by chosing from the
&quot;Structure -> Add residue&quot; menu. Common terminals motifs can
be added by chosing from the &quot;Structure -> Add terminal&quot;
menu. A residue can be inserted before the current selection by
clicking on &quot;Structure -> insert residue before&quot;.

<br><br>

The properties of a residue (such as anomeric state, chirality and
anomeric atom) and the position of the linkage to its predecessor can
be set using the dialog activated by &quot;Structure -> Residue
properties&quot;. The type of the reducing end of the selected
structure can be changed by clicking on &quot;Structure -> change
reducing end type&quot;. In this way labels and markers can be added
to the structure. The mass of the marker is added to the total mass of
the structure.

<br><br>

Fuzzy structures with uncertain antennae positions can be created by
adding a bracket to a selected structure with the &quot;Structure ->
Add bracket&quot; command. The antennae can then be added to the
structure by selecting the bracket and adding the desired residues.

<h2 align="left">Export to file</h2>

<p align="left">
The content of the structure panel can be saved to file, using the
internal string format, for later retrieval. Otherwise, the structure
drawings can be exported into file in several graphical formats
(PS,EPS,PDF,SVG,JPG,BMP,PNG,GIF) using the menu &quot;File -> Export
to graphical formats&quot;.

</p>

<h2 align="left">Selection and Navigation</h2>

<p align="left">
A single residue is selected by clicking the mouse left button on
it. If the &lt;ctrl&gt; button is pressed, the residues that are
already selected will remain in the same state, otherwise they will be
deselected. If the &lt;shift&gt; button is pressed all the residues on
the path connecting the last selection and the current one will be
selected as well. By pressing the mouse left button outside of any
residues and dragging it, the rectangle selection tool will be
activated. When the mouse button is released all the residues in the
rectangle area will be selected. If the &lt;ctrl&gt; button is
pressed, the residues that are already selected will remain in the
same state, otherwise they will be deselected. To select all residues
of all structures just press &gt;ctrl+A&lt; or go to &quot;Edit ->
Select all&quot;. The currently selected structure is the one
containing the last selected residue.

<br><br>

By clicking &lt;ctrl&gt; plus one of the arrow buttons the selection
is moved from the last selected residue to the nearest residue in the
direction indicated by the arrow. If no residue is selected, the
selection is placed on the reducing end of the first or the last
structure (depending on the arrow button).
</p>


<h2 align="left">Cut and Copy</h2>

<p align="left">
All the usual cut/copy/paste operations are implemented in the
GlycoWorkbench. The selected residues can be cut/copy from a location
and then pasted in a different location in the same window. If no
residues are selected when performing the &quot;paste&quot; action a
new structure will be created, otherwise the content of the clipboard
will be added to the last selected residue.  The selection can also be
pasted in a different window of the GlycoWorkbench. Finally, the
copied residues can be pasted as an image in a graphic editor or Word
document.
</p>

<h2 align="left">Drag and Drop</h2>

<p align="left">
By pressing the mouse left button on a single residue or a group of
selected residues, the drag and drop mode is activated. The selected
residues can be dragged to any part of the drawing canvas. When the
mouse button is released the dragged residues will be moved to the
final location. If the button is released upon an existing residue,
the selection will be added to it, otherwise a new structure will be
created containing the selected residues. If the &lt;ctrl&gt; button
is pressed the selection will be copied from the original location to
its destination, otherwise the selected residues will be deleted from
the original location. The selection cannot be dragged outside the
current drawing canvas.
</p>


<h2 align="left">Visualization Options</h2>

<p align="left">
The orientation of the drawn structure can be changed from
right-to-left to left-to-right, to bottom-to-top to top-to-bottom, by
clicking on &quot;Structure -> change orientation&quot;. The
orientation will affect also the way fragments are drawn in the
fragment panel. The cartoon notation used to represent structures can
be changed from the menu &quot;View&quot;. Currently, three notations
are supported: CFG standard, CFG black and white, Oxford. The
visualization of linkages information is controlled with the
&quot;View -> show linkage info&quot; command. In the same menu with
the command &quot;View -> show masses when exporting&quot; it is
possible to activate/deactivate the display of mass information in the
exported/printed structure drawings.

</p>

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